<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@font-face
        {font-family:Wingdings;
        panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
        {font-family:"Cambria Math";
        panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
        {font-family:Calibri;
        panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
        {font-family:"Lucida Sans Unicode";
        panose-1:2 11 6 2 3 5 4 2 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
        {margin:0cm;
        margin-bottom:.0001pt;
        font-size:11.0pt;
        font-family:"Calibri","sans-serif";
        mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
        {mso-style-priority:99;
        color:#0563C1;
        text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
        {mso-style-priority:99;
        color:#954F72;
        text-decoration:underline;}
p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
        {mso-style-priority:34;
        margin-top:0cm;
        margin-right:0cm;
        margin-bottom:0cm;
        margin-left:36.0pt;
        margin-bottom:.0001pt;
        font-size:11.0pt;
        font-family:"Calibri","sans-serif";
        mso-fareast-language:EN-US;}
span.EmailStyle17
        {mso-style-type:personal-compose;
        font-family:"Calibri","sans-serif";
        color:windowtext;}
.MsoChpDefault
        {mso-style-type:export-only;
        font-family:"Calibri","sans-serif";
        mso-fareast-language:EN-US;}
@page WordSection1
        {size:612.0pt 792.0pt;
        margin:70.85pt 70.85pt 70.85pt 70.85pt;}
div.WordSection1
        {page:WordSection1;}
/* List Definitions */
@list l0
        {mso-list-id:2119906178;
        mso-list-type:hybrid;
        mso-list-template-ids:-894791456 1752871314 67895299 67895301 67895297 67895299 67895301 67895297 67895299 67895301;}
@list l0:level1
        {mso-level-start-at:0;
        mso-level-number-format:bullet;
        mso-level-text:-;
        mso-level-tab-stop:none;
        mso-level-number-position:left;
        text-indent:-18.0pt;
        font-family:"Calibri","sans-serif";
        mso-fareast-font-family:Calibri;
        mso-bidi-font-family:"Times New Roman";}
@list l0:level2
        {mso-level-number-format:bullet;
        mso-level-text:o;
        mso-level-tab-stop:none;
        mso-level-number-position:left;
        text-indent:-18.0pt;
        font-family:"Courier New";}
@list l0:level3
        {mso-level-number-format:bullet;
        mso-level-text:\F0A7;
        mso-level-tab-stop:none;
        mso-level-number-position:left;
        text-indent:-18.0pt;
        font-family:Wingdings;}
@list l0:level4
        {mso-level-number-format:bullet;
        mso-level-text:\F0B7;
        mso-level-tab-stop:none;
        mso-level-number-position:left;
        text-indent:-18.0pt;
        font-family:Symbol;}
@list l0:level5
        {mso-level-number-format:bullet;
        mso-level-text:o;
        mso-level-tab-stop:none;
        mso-level-number-position:left;
        text-indent:-18.0pt;
        font-family:"Courier New";}
@list l0:level6
        {mso-level-number-format:bullet;
        mso-level-text:\F0A7;
        mso-level-tab-stop:none;
        mso-level-number-position:left;
        text-indent:-18.0pt;
        font-family:Wingdings;}
@list l0:level7
        {mso-level-number-format:bullet;
        mso-level-text:\F0B7;
        mso-level-tab-stop:none;
        mso-level-number-position:left;
        text-indent:-18.0pt;
        font-family:Symbol;}
@list l0:level8
        {mso-level-number-format:bullet;
        mso-level-text:o;
        mso-level-tab-stop:none;
        mso-level-number-position:left;
        text-indent:-18.0pt;
        font-family:"Courier New";}
@list l0:level9
        {mso-level-number-format:bullet;
        mso-level-text:\F0A7;
        mso-level-tab-stop:none;
        mso-level-number-position:left;
        text-indent:-18.0pt;
        font-family:Wingdings;}
ol
        {margin-bottom:0cm;}
ul
        {margin-bottom:0cm;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1027" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=FR link="#0563C1" vlink="#954F72"><div class=WordSection1><p class=MsoNormal>Hi all, <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span lang=EN-US>This is a bug or feature request depending on the point of views ;)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>The UMLS Semantic Network (STY in BioPortal) is not parsed completely:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><a href="http://bioportal.bioontology.org/ontologies/STY">http://bioportal.bioontology.org/ontologies/STY</a> <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Especially the hierarchy as described here: <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><a href="http://www.nlm.nih.gov/research/umls/META3_current_semantic_types.html">http://www.nlm.nih.gov/research/umls/META3_current_semantic_types.html</a><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>is not included.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Therefore, when filtering annotation with semantic types, the “hierarchy knowledge ” of the Semantic Network cannot be used.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>For instance: <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>When annotating “melanoma” and filtering with T147:”Disease or syndrome” I should get an annotation with </span><span lang=EN-US style='font-size:9.0pt;font-family:"Lucida Sans Unicode","sans-serif";color:#234979;background:#F5FAFA'><a href="http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F2092003">http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F2092003</a></span><span lang=EN-US style='font-size:9.0pt;font-family:"Lucida Sans Unicode","sans-serif";background:#F5FAFA'> which is “Malignant melanoma” in SNOMEDCT that actually has T191 (neoplastic process) which is defined in the UMLS SN has a subtype of T147.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Lucida Sans Unicode","sans-serif";background:#F5FAFA'>Currently the Annotator does not match anything if filtering with T147 is on.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Of course this should work also with all the parents in the hierarchy.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I see 2 bugs to fix: <o:p></o:p></span></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span lang=EN-US><span style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'>          </span></span></span><![endif]><span lang=EN-US>Parse the UMLS SN completely (has issued at: <a href="https://github.com/ncbo/umls2rdf/issues/9">https://github.com/ncbo/umls2rdf/issues/9</a>)<o:p></o:p></span></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span lang=EN-US><span style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'>          </span></span></span><![endif]><span lang=EN-US>Change Annotator code to use that hierarchy when filtering<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Hope it helps<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Clement<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>PS: as soon as I get a developer in Montpellier, we will do it ;)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span lang=EN-US style='mso-fareast-language:FR'>---------------------------------------------------------------------------------------------------------------------------<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='mso-fareast-language:FR'>Dr. <b>Clement JONQUET</b>  -  <i>PhD in Informatics  -  Assistant Professor<o:p></o:p></i></span></p><p class=MsoNormal><i><span lang=EN-US style='mso-fareast-language:FR'>PI of the <a href="http://www.lirmm.fr/sifr/"><span style='color:blue'>SIFR project</span></a>: Semantic Indexing of French Biomedical Data Resources (ANR, UM2, CNRS, IBC)<o:p></o:p></span></i></p><p class=MsoNormal><i><span lang=EN-US style='mso-fareast-language:FR'>Organizer of <a href="http://www.meetup.com/webscience-montpellier/"><span style='color:blue'>Web Science Montpellier</span></a> Meetup</span></i><span lang=EN-US style='mso-fareast-language:FR'><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='mso-fareast-language:FR'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='mso-fareast-language:FR'><a href="mailto:jonquet@lirmm.fr"><span style='color:blue'>jonquet@lirmm.fr</span></a><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='mso-fareast-language:FR'><a href="http://www.lirmm.fr/~jonquet"><span style='color:blue'>http://www.lirmm.fr/~jonquet</span></a> <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='mso-fareast-language:FR'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='mso-fareast-language:FR'>                <b>University of Montpellier</b>                          Tel:                      +33/4 67 14 97 43<b><o:p></o:p></b></span></p><p class=MsoNormal><span lang=EN-US style='mso-fareast-language:FR'>                LIRMM                                                            Fax:                     +33/4 67  41 85 00           <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='mso-fareast-language:FR'>                161 rue Ada                                                   Skype:                 clementpro<br>                34095 Montpellier Cdx 5                            Twitter:               <a href="http://twitter.com/jonquet_lirmm"><span style='color:blue'>@jonquet_lirmm</span></a><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='mso-fareast-language:FR'>                France                                                            Google:               <a href="mailto:jonquet.lirmm@gmail.com"><span style='color:blue'>jonquet.lirmm@gmail.com</span></a><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='mso-fareast-language:FR'>----------------------------------------------------------------------------------------------------------------------<o:p></o:p></span></p><p class=MsoNormal><!--[if gte vml 1]><v:shapetype id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t" path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
<v:stroke joinstyle="miter" />
<v:formulas>
<v:f eqn="if lineDrawn pixelLineWidth 0" />
<v:f eqn="sum @0 1 0" />
<v:f eqn="sum 0 0 @1" />
<v:f eqn="prod @2 1 2" />
<v:f eqn="prod @3 21600 pixelWidth" />
<v:f eqn="prod @3 21600 pixelHeight" />
<v:f eqn="sum @0 0 1" />
<v:f eqn="prod @6 1 2" />
<v:f eqn="prod @7 21600 pixelWidth" />
<v:f eqn="sum @8 21600 0" />
<v:f eqn="prod @7 21600 pixelHeight" />
<v:f eqn="sum @10 21600 0" />
</v:formulas>
<v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect" />
<o:lock v:ext="edit" aspectratio="t" />
</v:shapetype><v:shape id="Group_x0020_2" o:spid="_x0000_s1026" type="#_x0000_t75" style='position:absolute;margin-left:14.25pt;margin-top:76.5pt;width:381.75pt;height:39pt;z-index:251659264;visibility:visible;mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:9pt;mso-wrap-distance-top:0;mso-wrap-distance-right:9pt;mso-wrap-distance-bottom:0;mso-position-horizontal:absolute;mso-position-horizontal-relative:char;mso-position-vertical:absolute;mso-position-vertical-relative:line;mso-width-percent:0;mso-height-percent:0;mso-width-relative:page;mso-height-relative:page'>
<o:lock v:ext="edit" aspectratio="f" />
<w:wrap anchory="line"/>
<w:anchorlock/>
</v:shape><![endif]--><![if !vml]><span style='mso-ignore:vglayout'><table cellpadding=0 cellspacing=0 align=left><tr><td width=19 height=102></td></tr><tr><td></td><td><img width=509 height=52 src="cid:image001.png@01CF9C5E.52EB1270" v:shapes="Group_x0020_2"></td></tr></table></span><![endif]><span lang=EN-US style='mso-fareast-language:FR'><o:p> </o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:FR'><o:p> </o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div></body></html>